He uses Nvidia graphics chips often used in consoles and PCs to
perform a number of simulations, including that of the bacterial
ribosome, with the goal of understanding how to develop
antibiotics that specifically target certain bacteria. He is also
simulating protein-nanoparticle interactions. Which are small but
computationally-challenging to simulate due to the many
interactions involved.

The types of simulations that Cho and his team are doing have
been around for a while, but without the processing power of
graphics cards they can take much longer. "We are now able to look
at the entire biomolecule and even interactions between multiple
biomolecules -- something that would be impossible by current
standards using regular computers," Cho explained to
Wired.co.uk.

Cho's most recent simulation is of a
critical RNA molecule that forms part of an enzyme (telomerase)
that is found only in cancerous cells. Telomerase adds tiny molecules called
telomeres to the ends of DNA strands when cells divide, preventing
the cells from dying. "By knowing how telomerase folds and
functions, we provide a new area for researching cancer
treatments."

Cho told Wired.co.uk: "We are certainly not the first to try
using graphics cards for high performance computing, and there have
been successes in the literature in areas such as high energy
physics, bioinformatics, and even finance. At the core of this
technology is that graphics cards are fantastic for floating-point
calculations for each pixel on a screen. Mathematically, this is
exactly what happens on a biomolecular simulation except that we
are calculating physical interactions instead of pixels."

The proliferation of games consoles means that graphics processing units have come down in cost and risen in
power significantly. "We are now able to tackle much larger systems
and we are able to perform the simulations for much longer
timescales that can be directly compared to experiments by using
the graphics technology to perform our simulations," he said.

While there are lots of researchers who recognise the importance
of GPUs for scientific computing, a major bottleneck is developing
new algorithms and codes for programming on GPUs. Cho explains:
"While some problems are extraordinarily easy to implement on GPUs,
others are not so straightforward. This is why a strong background
in computer science, as well as biophysics, is necessary to solves
these problems well. That is why I am fortunate to have physics and
computer science graduate and undergraduate students work together
to solve these problems with me."

This isn't the first time games consoles have been involved in
medical research, however. Since 2007, Sony's PlayStation 3 has
supported the Folding@Home project from
Stanford University. By utilising spare computing cycles when the
console isn't being used for games, its processors can join a
network of machines around the world that simulate protein folding.
This helps researchers better understand Alzheimer's, Parkinson's
and various cancers.